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YMa-lab / CARD

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How to keep all the Spatial data? #56

Closed Smilenone closed 3 months ago

Smilenone commented 9 months ago

When running CARD, there are some of the pixels removed. How to keep the Spatial data?

YingMa0107 commented 9 months ago

Hi @Smilenone,

Thank you for your interest in our package.

You can try to set the minCountGene = 0 when you create the CARD object, then it should keep all the spatial locations.

Best, Ying

cynthier commented 7 months ago

@YingMa0107 Hi, Ying, I set 

minCountGene = 0,
minCountSpot = 0

but after creating object, 200~300 spots will be removed.

YMalab commented 4 months ago

@cynthier

This could be due to CARD taking into account the common genes between scRNA-seq and SRT data, and removing the spots if there is no expression across all those common genes.

Best, Ying